Figure 1.

V-plots reveal chromatin features of transcription factor binding sites. (a) V-plot of MNase-seq data from Kent et al. [17] centered on binding sites for the Cbf1 transcription factor. Figure adapted from
Henikoff et al. [20]. (b) Interpretive diagram of a V-plot. A dot representing the midpoint of each paired-end
fragment is placed on the graph. Its Y-axis value represents its length and its X-axis
value represents the distance of its midpoint from the center of a given genomic feature
(in this case, a transcription factor binding site (TFBS)). Locations of dots corresponding
to each fragment are indicated by red arrows. The minimal region protected by the
transcription factor (TF) is indicated by the intersection of the left and right diagonals
on the Y-axis and also as the width of the gap on the X-axis resulting from extrapolation
of the diagonals to Y = 0. The left diagonal results from fragments cleaved precisely
to the right of the TF-protected region, and the converse is true of the right diagonal.
The triangular densities flanking the TF-protected region are generated by protected
regions adjacent to the TFBS that are cleaved between the TFBS and the protein responsible
for the density.